| Previous changeset 58:0e592dcaeb7f (2024-03-21) Next changeset 60:81d535970196 (2024-03-25) |
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Commit message:
planemo upload for repository https://github.com/usegalaxy-eu/temporary-tools/tree/master/jbrowse2 commit faada92caf5aaabe58e52b161687a30d542a07b9 |
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modified:
jbrowse2.py jbrowse2.xml macros.xml |
| b |
| diff -r 0e592dcaeb7f -r f807e219cec3 jbrowse2.py --- a/jbrowse2.py Thu Mar 21 09:06:52 2024 +0000 +++ b/jbrowse2.py Fri Mar 22 22:04:08 2024 +0000 |
| [ |
| b'@@ -439,11 +439,13 @@\n if trackDict.get("displays", None): # use first if multiple like bed\n style_data["type"] = trackDict["displays"][0]["type"]\n style_data["displayId"] = trackDict["displays"][0]["displayId"]\n- return {\n+ wstyle = {\n "displays": [\n style_data,\n ]\n }\n+ logging.warn("style=%s" % (wstyle))\n+ return wstyle\n \n def process_genomes(self):\n assemblies = []\n@@ -496,16 +498,16 @@\n "type": "BgzipFastaAdapter",\n "fastaLocation": {\n "uri": faname,\n- "locationType": "UriLocation",\n+ "locationType": "UriLocation"\n },\n "faiLocation": {\n "uri": faname + ".fai",\n- "locationType": "UriLocation",\n+ "locationType": "UriLocation"\n },\n "gziLocation": {\n "uri": faname + ".gzi",\n- "locationType": "UriLocation",\n- },\n+ "locationType": "UriLocation"\n+ }\n }\n else:\n faname = gname + ".fa.gz"\n@@ -528,7 +530,7 @@\n },\n "gziLocation": {\n "uri": faname + ".gzi",\n- },\n+ }\n }\n \n trackDict = {\n@@ -538,7 +540,6 @@\n "trackId": gname,\n "adapter": adapter,\n },\n- "rendering": {"type": "DivSequenceRenderer"},\n "displays": [\n {\n "type": "LinearReferenceSequenceDisplay",\n@@ -548,7 +549,7 @@\n "type": "LinearGCContentDisplay",\n "displayId": "%s-LinearGCContentDisplay" % gname,\n },\n- ],\n+ ]\n }\n return trackDict\n \n@@ -635,6 +636,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -708,6 +711,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n if self.config_json.get("plugins", None):\n@@ -781,6 +786,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n os.unlink(gff3)\n@@ -827,6 +834,8 @@\n }\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -880,6 +889,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -928,6 +939,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -980,6 +993,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -1041,6 +1056,8 @@\n },\n ],\n }\n+ style_json = self._prepare_track_style(trackDict)\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n '..b'- # trouble from spacey names in command lines avoidance\n- if gname not in self.genome_names:\n- # ignore if already there - eg for duplicates among pafs.\n- useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(\n- "https://"\n- )\n- asstrack = self.make_assembly(pgpaths[i], gname, useuri)\n- self.genome_names.append(gname)\n- if self.config_json.get("assemblies", None):\n- self.config_json["assemblies"].append(asstrack)\n- else:\n- self.config_json["assemblies"] = [\n- asstrack,\n- ]\n+ passnames.append(gname)\n+ # trouble from spacey names in command lines avoidance\n+ if gname not in self.genome_names:\n+ # ignore if already there - eg for duplicates among pafs.\n+ useuri = pgpaths[i].startswith("http://") or pgpaths[i].startswith(\n+ "https://"\n+ )\n+ asstrack = self.make_assembly(pgpaths[i], gname, useuri)\n+ self.genome_names.append(gname)\n+ if self.config_json.get("assemblies", None):\n+ self.config_json["assemblies"].append(asstrack)\n+ else:\n+ self.config_json["assemblies"] = [\n+ asstrack,\n+ ]\n url = "%s.paf" % (trackData["label"])\n dest = "%s/%s" % (self.outdir, url)\n self.symlink_or_copy(os.path.realpath(data), dest)\n@@ -1131,18 +1151,16 @@\n "type": "PAFAdapter",\n "pafLocation": {"uri": url},\n "assemblyNames": passnames,\n- },\n- "displays": [\n- {\n- "type": "LinearSyntenyDisplay",\n- "displayId": "%s-LinearSyntenyDisplay" % tId,\n- },\n- {\n- "type": "DotPlotDisplay",\n- "displayId": "%s-DotPlotDisplay" % tId,\n- },\n- ],\n+ }\n }\n+ style_json = {\n+ "displays": [\n+ { "type": "LinearBasicDisplay",\n+ "displayId": "%s-LinearBasicyDisplay" % trackDict["trackId"]\n+ }\n+ ]\n+ }\n+ trackDict["style"] = style_json\n self.tracksToAdd.append(trackDict)\n self.trackIdlist.append(tId)\n \n@@ -1284,7 +1302,6 @@\n if "displays" in track_conf:\n disp = track_conf["displays"][0]["type"]\n style_data["type"] = disp\n- style_data["configuration"] = "%s-%s" % (tId, disp)\n if track_conf.get("style_labels", None):\n # TODO fix this: it should probably go in a renderer block (SvgFeatureRenderer) but still does not work\n # TODO move this to per track displays?\n@@ -1296,7 +1313,6 @@\n "displays": [style_data],\n }\n )\n-\n # The view for the assembly we\'re adding\n view_json = {"type": "LinearGenomeView", "tracks": tracks_data}\n \n@@ -1534,9 +1550,6 @@\n }\n else:\n track_conf["style"] = {}\n- tst = track_conf["style"].get("type", None)\n- if tst:\n- track_conf["style"]["configuration"] = "%s-%s" % (track_conf["label"], tst)\n if track.find("options/style_labels"):\n track_conf["style_labels"] = {\n item.tag: parse_style_conf(item)\n@@ -1565,6 +1578,7 @@\n default_session_data["session_name"] = root.find(\n "metadata/general/session_name"\n ).text\n+ logging.warn("default_session=%s" % (default_session_data))\n jc.zipOut = root.find("metadata/general/zipOut").text == "true"\n general_data = {\n "analytics": root.find("metadata/general/analytics").text,\n' |
| b |
| diff -r 0e592dcaeb7f -r f807e219cec3 jbrowse2.xml --- a/jbrowse2.xml Thu Mar 21 09:06:52 2024 +0000 +++ b/jbrowse2.xml Fri Mar 22 22:04:08 2024 +0000 |
| [ |
| @@ -139,16 +139,17 @@ #for $tg in $track_groups: #for $track in $tg.data_tracks: #if $track.data_format.useuri.insource == "uri": - <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> - <files> - <trackFile path="${track.data_format.useuri.annouri}" ext="${track.data_format.data_format_select}" label="${track.data_format.useuri.annoname}" useuri="yes"> - <metadata> - <dataset id = "${track.data_format.useuri.annouri}" /> - </metadata> - </trackFile> - </files> - <options/> - </track> + <track cat="${tg.category}" format="paf" visibility="${track.data_format.track_visibility}"> + <files> + <trackFile path="${ $track.data_format.useuri.insource.annouri}" ext="paf" + label="${track.data_format.useuri.insource.annoname}" useuri="yes"> + <metadata> + <dataset id = "${track.data_format.useuri.insource.annouri}" /> + </metadata> + </trackFile> + </files> + <options/> + </track> #else if $track.data_format.useuri.insource == "history": #if $track.data_format.useuri.annotation: <track cat="${tg.category}" format="${track.data_format.data_format_select}" visibility="${track.data_format.track_visibility}"> @@ -203,7 +204,10 @@ #end if #end if #if str($track.data_format.data_format_select) in ["bam", "cram"]: - <type>"LinearAlignmentsDisplay"</type> + <type>LinearAlignmentsDisplay</type> + #end if + #if str($track.data_format.data_format_select) in ["paf"]: + <type>LinearBasicDisplay</type> #end if </style> #if str($track.data_format.data_format_select) == "bam": @@ -235,13 +239,13 @@ #else if str($track.data_format.data_format_select) == "paf": <paf> <genome> - #for gnome in $track.data_format.synteny_genome: - $gnome, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annotation, #end for </genome> <genome_label> - #for gnome in $track.data_format.synteny_genome: - $gnome.name, + #for refgenome in $track.data_format.pafuseuri.refgenomes: + $refgenome.annoname, #end for </genome_label> </paf> @@ -327,17 +331,17 @@ <repeat name="data_tracks" title="Annotation Track"> <conditional name="data_format" label="Track Data Selection Options"> <param type="select" label="Track Type" name="data_format_select"> - <option value="bam">BAM Pileup track</option> + <option value="bam">BAM track. Recommend convert to faster BED unless mapping annotation needed</option> <option value="bed">BED track</option> <option value="bigwig">BigWig track</option> - <option value="blastxml">Blast XML track - converted to GFF</option> + <option value="blastxml">Blast XML track (as GFF3)</option> + <option value="cram">CRAM track. Currently not advantageous over BAM in Galaxy. Convert to BED like BAM.</option> + <option value="gff">GFF/GFF3 track</option> <option value="cool">HiC as cool/mcool/scool format files</option> - <option value="cram">CRAM</option> - <option value="gff">GFF/GFF3 feature track</option> <option value="hic">HiC as juicebox_hic format file. Tabular hic_matrix will NOT work.</option> <option value="maf">Multiple alignment format. Reference name must match the MAF name exactly to work correctly</option> <option value="paf">PAF - approximate mapping positions between two set of sequences</option> - <option value="vcf">VCF SNP</option> + <option value="vcf">VCF SNP track</option> </param> <when value="blastxml"> <expand macro="input_conditional" label="BlastXML Track Data" format="blastxml" /> @@ -411,12 +415,10 @@ <expand macro="track_visibility" /> </when> <when value="paf"> - <param label="Comparison genome sequence" help="Paf from these as the reference(s), using the common reference as the reads to map" - format="fasta" - name="synteny_genome" - type="data" - multiple="True"/> - <expand macro="input_conditional" label="Synteny data" format="paf" help="Make paf with mashmap or minimap2 mapping real reference onto desired syntenic references"/> + <expand macro="input_conditional" label="PAF format synteny mapping data" format="paf" + help="PAF made with mashmap or minimap2 mapping the real reference as a query on the comparison genomes as references"/> + <expand macro="pafref_conditional" label="Comparison genome sequence(s)" + format="fasta" help="Paf from these as the reference(s), using the common reference as the reads to map"/> <expand macro="track_visibility" /> </when> |
| b |
| diff -r 0e592dcaeb7f -r f807e219cec3 macros.xml --- a/macros.xml Thu Mar 21 09:06:52 2024 +0000 +++ b/macros.xml Fri Mar 22 22:04:08 2024 +0000 |
| b |
| @@ -522,7 +522,7 @@ <param name="insource" type="select" label="Define track data as a history file or an internet URI" help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> <option value="history" selected="true">Track data from a history file</option> - <option value="uri" selected="true">Tabix data URI - index files must be available at corresponding URI</option> + <option value="uri" >Tabix data URI - index files must be available at corresponding URI</option> </param> <when value="history"> <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> @@ -539,6 +539,39 @@ </when> </conditional> </xml> + <xml name="pafref_conditional" token_label="Track Data" token_format="data"> + <conditional name="pafuseuri"> + <param name="insource" type="select" label="PAF reference data from a history file or an internet URI?" + help="A public URI implies that all the associated tabix files are also in place. They are created for history files"> + <option value="history" selected="true">PAF genome reference data from a history file</option> + <option value="uri">PAF genome reference data from tabix data URI - index files must be available at corresponding URI</option> + </param> + <when value="history"> + <repeat name="refgenomes" title="Add one or more comparison genomes used to make the PAF"> + <param label="@LABEL@" format="@FORMAT@" name="annotation" multiple="True" optional="true" type="data" /> + <param label="Short name for track display" name="annoname" type="text" > + <sanitizer invalid_char="_"> + <valid initial="string.printable" > + <remove value="'" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + <when value="uri"> + <repeat name="refgenomes" title="Provide URI for a comparison genomesused to make the PAF"> + <param label="@LABEL@" name="annotation" type="text" /> + <param label="Short name for track display" name="annoname" type="text" > + <sanitizer invalid_char="_"> + <valid initial="string.printable" > + <remove value="'" /> + </valid> + </sanitizer> + </param> + </repeat> + </when> + </conditional> + </xml> <xml name="citations"> <citations> <citation type="doi">10.1186/s13059-016-0924-1</citation> |